核酸碱基与甘氨酸二肽间氢键作用的最佳位点

优化得到了碱基腺嘌呤、胸腺嘧啶、尿嘧啶、鸟嘌呤及胞嘧啶与甘氨酸二肽分子形成的28个氢键复合物的稳定结构并计算了结合能, 探讨了五种碱基与甘氨酸二肽分子间氢键作用的最佳位点. 本文研究发现: 每种碱基均可以通过不同位点与二肽分子形成氢键复合物, 腺嘌呤、胸腺嘧啶、尿嘧啶、鸟嘌呤及胞嘧啶分别最倾向使用A3、T1、U1、G3及C1位点与甘氨酸二肽分子形成氢键复合物; 碱基分子某位点的质子化反应焓变越负所形成的氢键复合物越稳定, 去质子化反应焓变越小所形成的氢键复合物越稳定; 由氢键复合物的结合能计算得到的稳定性次序与由碱基分子质子化和去质子化反应焓变推得的稳定性次序一致.     

配体间相互作用研究: 氨基酸与二肽配体形成 质子复合物的稳定性

用pH电位滴定法测定了苯丙氨酰亮氨酸(PL)与甘氨酸(Gly)、丙氨酸(Ala)、缬氨酸(Val)、亮氨酸(Leu)、异亮氨酸(Ile)、苯丙氨酸(Phe)在离子强度为0.1mol/L(NaNO~3),(25.0±0.1)℃时形成质子复合物的稳定常数,并对苯丙氨酰亮氨酸与六种氨基酸相互作用体系进行了量子化学和分子力学计算。从配体间弱相互作用的观点,讨论了二肽配体对氨基酸分子的识别。结果表明,二肽与氨基酸配体间的结合主要受到配体间静电、氢键作用的控制,同时受到范德华力和键间排斥能等弱相互作用的影响。     

配体间相互作用研究: 氨基酸与二肽配体形成 质子复合物的稳定性

用pH电位滴定法测定了苯丙氨酰亮氨酸(PL)与甘氨酸(Gly)、丙氨酸(Ala)、缬氨酸(Val)、亮氨酸(Leu)、异亮氨酸(Ile)、苯丙氨酸(Phe)在离子强度为0.1mol/L(NaNO~3),(25.0±0.1)℃时形成质子复合物的稳定常数,并对苯丙氨酰亮氨酸与六种氨基酸相互作用体系进行了量子化学和分子力学计算。从配体间弱相互作用的观点,讨论了二肽配体对氨基酸分子的识别。结果表明,二肽与氨基酸配体间的结合主要受到配体间静电、氢键作用的控制,同时受到范德华力和键间排斥能等弱相互作用的影响。     

取代基对1-甲基尿嘧啶与N-甲基乙酰胺氢键复合物中氢键强度的影响

使用密度泛函理论B3LYP方法和二阶微扰理论MP2方法对由1-甲基尿嘧啶与N-甲基乙酰胺所形成的氢键复合物中的氢键强度进行了理论研究, 探讨了不同取代基取代氢键受体分子1-甲基尿嘧啶中的氢原子对氢键强度的影响和氢键的协同性. 研究表明: 供电子取代基使N－H…O＝C氢键键长r(H…O)缩短, 氢键强度增强; 吸电子取代基使N－H…O＝C氢键键长r(H…O)伸长, 氢键强度减弱. 自然键轨道(NBO)分析表明: 供电子基团使参与形成氢键的氢原子的正电荷增加, 使氧原子的负电荷增加, 使质子供体和受体分子间的电荷转移量增多; 吸电子基团则相反. 供电子基团使N－H…O＝C氢键中氧原子的孤对电子轨道n(O)对N－H的反键轨道σ^*(N－H)的二阶相互作用稳定化能增强, 吸电子基团使这种二阶相互作用稳定化能减弱. 取代基对与其相近的N－H…O＝C氢键影响更大.     

N,N-二甲基乙酰胺与醇分子间相互作用的理论研究

采用密度泛函理论在B3LYP/6-311＋G*水平上对乙醇、丙醇、丁醇、戊醇与N,N-二甲基乙酰胺形成的1∶1氢键复合物进行计算研究. 结果表明: 醇与N,N-二甲基乙酰胺形成的复合物存在强的氢键, 表现为羰基氧原子的孤对电子与醇羟基反键σ轨道的相互作用. 振动分析显示, 分子间C＝O…H—O氢键的形成使C＝O和H—O伸缩振动频率明显红移. 溶剂对氢键产生较大的影响, 随着溶剂极性的增加, 复合物氢键有蓝移趋势.     

取代基对腺嘌呤与胸腺嘧啶氢键复合物体系结合能的影响

优化得到了17个取代胸腺嘧啶与腺嘌呤形成的氢键复合物的结构, 并计算了这些复合物的结合能, 探讨了胸腺嘧啶上不同取代基对结合能的影响. 结果表明, CF₃取代的胸腺嘧啶与腺嘌呤间的结合能大于胸腺嘧啶与腺嘌呤间的结合能, 这可能是屈氟尿苷具有阻止病毒及肿瘤扩散功能的原因所在. SO₃H, CN和NO₂取代的胸腺嘧啶与腺嘌呤间具有更大的结合能, 表明这3个基团取代的胸腺嘧啶也可能具有潜在的抗肿瘤作用. 分子中原子理论与自然键轨道分析表明, 在所有体系中, 氢键N—H…N最强, N—H…O=C次之, C—H…O=C最弱, 轨道作用在氢键作用中占有重要地位.     

七水氯化铈与甘氨酸丙氨酸三元固态配合物的热化学

合成了Ce3+与甘氨酸丙氨酸混配体配合物, 通过红外光谱分析、元素分析、热重分析和化学分析, 确定了配合物的组成为Ce(Gly)2(Ala)3Cl3*2H2O, 并用溶解量热法分别测定了CeCl3*7H2O(s), 2Gly(s)+3Ala(s)和Ce(Gly)2(Ala)3Cl3*2H2O(s)在2 mol*L-1 HCl中的溶解焓; 再根据盖斯定律设计了一个热化学循环, 计算得到了七水氯化铈与甘氨酸丙氨酸反应的反应焓ΔrHmθ (298.15 K)=29.075 kJ*mol-1, 并求出了Ce(Gly)2(Ala)3Cl3*2H2O(s)标准生成焓△fHmθ [Ce(Gly)2(Ala)3Cl3*2H2O, s, 298.15 K]=-4468.0 kJ*mol-1.     

槲皮素与腺嘌呤氢键作用的最佳位点

本文优化得到了16个由槲皮素与腺嘌呤形成的氢键复合物的稳定结构,并计算了它们的结合能.研究发现,在气相和水相中,槲皮素均通过qu1位点与腺嘌呤作用形成稳定的氢键复合物.比较了腺嘌呤与槲皮素形成的氢键复合物、腺嘌呤与胸腺嘧啶形成的Watson-Crick碱基对的相对稳定性.在气相条件下Watson-Crick碱基对更稳定,在水相条件下腺嘌呤与槲皮素形成的氢键复合物更稳定,说明水相条件下腺嘌呤与槲皮素之间的相互作用强于与胸腺嘧啶之间的相互作用.基于标准反应Gibbs自由能变的计算结果估算了水相条件下腺嘌呤与槲皮素形成的氢键复合物和Watson-Crick碱基对的相对平衡浓度.     

310.15K时蛋白质模型化合物与二元醇在水溶液中的异系焓相互作用

利用2277热活性检测仪的流动量热系统测量蛋白质模型化合物(甘氨酸、丙基酸、N,N-二甲基甲酰胺(DMF)和N,N-二甲基乙酰胺(DMA))与二元醇(1,3-丁二醇和2,3-丁二醇)的混合过程焓变以及各自的稀释焓;依据McMillan-Mayer理论对实验数据进行分析,获得310.15K时水溶液中蛋白质模型化合物与二元醇异构体分子的异系焓相互作用系数(hxy,hxxy,hxyy).结果表明,hxy值均为正值,此过程吸热效应占主导作用,并且hxy(DMA)hxy(丙氨酸)hxy(甘氨酸)hxy(DMF)和hxy(2,3-丁二醇)hxy(1,3-丁二醇).根据结果讨论了溶质-溶质相互作用和溶质-溶剂相互作用情况,阐明了二元醇官能团相对位置的变化对hxy值的影响,发现DMF或DMA与二元醇之间有较强的氢键作用,由于DMF分子共振结构有较好的可极化性,DMF与二元醇的氢键作用被进一步加强.     

吡啶与HCl和CHCl3形成分子间红移氢键和蓝移氢键的理论研究

采用量子化学从头算的MP2方法, 分别在6-31G(d,p), 6-311+G(d,p)和AUG-cc-pVDZ基组下, 研究了复合物C5H5N…HCl(1), C5H5N…HCCl3(2)和C5H5N…HCCl3(3)的分子间氢键. 计算结果表明, 在复合物1中, HCl中Cl—H键伸长, 形成Cl—H…N红移氢键; 在复合物2中, HCCl3中C—H键伸长, 形成C—H…N 红移氢键; 在复合物3中, HCCl3中C—H键收缩, 形成C—H…π蓝移氢键. 自然键轨道(NBO)分析表明, 影响氢键红移和氢键蓝移主要有3个因素: n(Y)→σ*(X—H)超共轭作用、X—H键轨道再杂化和质子供体电子密度重排. 其中, 超共轭作用属于键伸长效应, 电子密度重排和轨道再杂化属于键收缩效应. 在复合物1和2中, 由于键伸长效应处于优势地位导致形成红移氢键; 在复合物3中, 由于键收缩效应处于优势地位导致形成蓝移氢键.     

取代基对腺嘌呤与胸腺嘧啶氢键复合物体系结合能的影响简

优化得到了17个取代胸腺嘧啶与腺嘌呤形成的氢键复合物的结构,并计算了这些复合物的结合能,探讨了胸腺嘧啶上不同取代基对结合能的影响. 结果表明,CF3取代的胸腺嘧啶与腺嘌呤间的结合能大于胸腺嘧啶与腺嘌呤间的结合能,这可能是屈氟尿苷具有阻止病毒及肿瘤扩散功能的原因所在. SO3H,CN和NO2取代的胸腺嘧啶与腺嘌呤间具有更大的结合能,表明这3个基团取代的胸腺嘧啶也可能具有潜在的抗肿瘤作用. 分子中原子理论与自然键轨道分析表明,在所有体系中,氢键N—H…N最强,N—H…O=C次之,C—H…O=C最弱,轨道作用在氢键作用中占有重要地位.     

Structural and energetic effects in the molecular recognition of amino acids by 18-crown-6

Absolute 18-crown-6 (18C6) affinities of five amino acids (AAs) are determined using guided ion beam tandem mass spectrometry techniques. The AAs examined in this work include glycine (Gly), alanine (Ala), lysine (Lys), histidine (His), and arginine (Arg). Theoretical electronic structure calculations are performed to determine stable geometries and energetics for neutral and protonated 18C6 and the AAs as well as the proton bound complexes comprised of these species, (AA)H(+)(18C6). The proton affinities (PAs) of Gly and Ala are lower than the PA of 18C6, whereas the PAs of Lys, His, and Arg exceed that of 18C6. Therefore, the collision-induced dissociation (CID) behavior of the (AA)H(+)(18C6) complexes differs markedly across these systems. CID of the complexes to Gly and Ala produces H(+)(18C6) as the dominant and lowest energy pathway. At elevated energies, H(+)(AA) was produced in competition with H(+)(18C6) as a result of the relatively favorable entropy change in the formation of H(+)(AA). In contrast, CID of the complexes to the protonated basic AAs results in the formation of H(+)(AA) as the only direct CID product. H(+)(18C6) was not observed, even at elevated energies, as a result of unfavorable enthalpy and entropy change associated with its formation. Excellent agreement between the measured and calculated (AA)H(+)-18C6 bond dissociation energies (BDEs) is found with M06 theory for all complexes except (His)H(+)(18C6), where theory overestimates the strength of binding. In contrast, B3LYP theory significantly underestimates the (AA)H(+)-18C6 BDEs in all cases. Among the basic AAs, Lys exhibits the highest binding affinity for 18C6, suggesting that the side chains of Lys residues are the preferred binding site for 18C6 complexation in peptides and proteins. Gly and Ala exhibit greater 18C6 binding affinities than Lys, suggesting that the N-terminal amino group provides another favorable binding site for 18C6. Trends in the 18C6 binding affinities among the five AAs examined here exhibit an inverse correlation with the polarizability and proton affinity of the AA. Therefore, the ability of the N-terminal amino group to compete for 18C6 complexation is best for Gly and should become increasing less favorable as the size of the side chain substituent increases.     

带电组氨酸侧链与DNA碱基间非键作用强度的理论研究

采用MP2方法和6-31+G(d,p)基组优化得到了带有一个正电荷的组氨酸侧链与4个DNA碱基间形成的18个氢键复合物的气相稳定结构, 从文献中获取了组氨酸侧链与DNA碱基间形成的12个堆积和T型复合物的气相稳定结构, 使用包含基组重叠误差(BSSE)校正的MP2方法和aug-cc-pVTZ基组及密度泛函理论M06-2X-D3方法和aug-cc-pVDZ基组计算了这些复合物的结合能. 研究结果表明, 包含BSSE校正的M06-2X-D3方法和aug-cc-pVDZ基组能够给出较准确的结合能; 气相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用明显强于堆积作用和T型作用, 组氨酸侧链最易通过离子氢键与胞嘧啶C和鸟嘌呤G作用形成氢键复合物, 组氨酸与胞嘧啶C和鸟嘌呤G间的T型作用强于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用; 水相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用仍明显强于堆积作用和T型作用, 组氨酸侧链更易与胞嘧啶C和鸟嘌呤G相互作用形成氢键复合物, 但是最强的组氨酸侧链与胞嘧啶C间的T型作用明显弱于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用, 说明水相条件下组氨酸侧链与DNA碱基间主要通过离子氢键作用形成氢键复合物.     

An analytic potential energy function for the amide–amide and amide–water intermolecular hydrogen bonds in peptides

An analytic potential energy function is proposed and applied to evaluate the amide–amide and amide–water hydrogen‐bonding interaction energies in peptides. The parameters in the analytic function are derived from fitting to the potential energy curves of 10 hydrogen‐bonded training dimers. The analytic potential energy function is then employed to calculate the N? H…O?C, C? H…O?C, N? H…OH₂, and C?O…HOH hydrogen‐bonding interaction energies in amide–amide and amide–water dimers containing N‐methylacetamide, acetamide, glycine dipeptide, alanine dipeptide, N‐methylformamide, N‐methylpropanamide, N‐ethylacetamide and/or water molecules. The potential energy curves of these systems are therefore obtained, including the equilibrium hydrogen bond distances R(O…H) and the hydrogen‐bonding energies. The function is also applied to calculate the binding energies in models of β‐sheets. The calculation results show that the potential energy curves obtained from the analytic function are in good agreement with those obtained from MP2/6‐31+G** calculations by including the BSSE correction, which demonstrate that the analytic function proposed in this work can be used to predict the hydrogen‐bonding interaction energies in peptides quickly and accurately. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Halbsandwich‐Komplexe von Ruthenium(II), Rhodium(III) und Iridium(III) mit Tripeptidestern aus α‐, β‐ und γ‐Aminosäuren als Liganden. — Peptidsynthese und Cyclisierung zu Cyclotripeptiden am Metallzentrum

Metal Complexes with Biological Important Ligands. CXLII. Half Sandwich Complexes of Ruthenium(II), Rhodium(III), and Iridium(III) with Tripeptide Esters from α‐, β‐, and γ‐Amino Acids as Ligands. — Peptide Synthesis and Cyclization to Cyclotripeptides at Metal Centers Halfsandwich complexes of ruthenium, rhodium and iridium with deprotonated N, N', N"‐tripeptide ester ligands were obtained from chloro bridged compounds and tripeptide methyl esters ( 1—6 ) or by peptide synthesis at a metal centre ( 9—15 ). For the peptide synthesis at the complex (C₆Me₆)Ru coordinated dipeptide methyl esters from glycine and β‐alanine or γ‐amino butyric acid were elongated by an a‐amino acid methylester. The tripeptide ester Ru(η⁶‐C₆Me₆) complexes with chiral amino acid components and an “asymmetric” metal atom are formed with high diastereoselectivity. The tripeptide esters Gly‐Gly‐β‐AlaOMe, Val‐Gly‐β‐AlaOMe and Phe‐Gly‐β‐AlaOMe can be condensated at the (C₆Me₆)Ru complex with sodium methanolate to give triple deprotonated cyclic tripeptides.     

多相酶膜反应器合成生物活性二肽

生物活性肽;多相酶膜反应器合成生物活性二肽     

Complexes of Formaldehyde and α-Dicarbonyls with Hydroxylamine: FTIR Matrix Isolation and Theoretical Study

The interactions of formaldehyde (FA), glyoxal (Gly) and methylglyoxal (MGly) with hydroxylamine (HA) isolated in solid argon and nitrogen were studied using FTIR spectroscopy and ab initio methods. The spectra analysis indicates the formation of two types of hydrogen-bonded complexes between carbonyl and hydroxylamine in the studied matrices. The cyclic planar complexes are stabilized by O–H⋯O(C), and C–H⋯N interactions and the nonplanar complexes are stabilized by O–H⋯O(C) bond. Formaldehyde was found to form with hydroxylamine, the cyclic planar complex and methylglyoxal, the nonplanar one in both argon and nitrogen matrices. In turn, glyoxal forms with hydroxylamine the most stable nonplanar complex in solid argon, whereas in solid nitrogen, both types of the complex are formed.     

离子液体1-乙基-3-甲基咪唑三氟甲基磺酸盐与水之间的氢键作用

通过衰减全反射红外（ATR-IR）光谱、二维红外相关谱结合量子化学计算研究了1-乙基-3-甲基咪唑三氟甲基磺酸盐（[emim][OTf]）和水之间的氢键作用. 结果表明,在[emim][OTf]^-水体系中,当水的浓度较低时（0.1< x（D₂O）< 0.3）,水分子的主要存在形式是包裹在离子液体中的没有缔合的单体. 水分子优先填充到[emim][OTf]的空隙中,并且与[emim][OTf]的阴离子形成“[OTf]^-…HOH…[OTf]^-”结构,水分子与[emim][OTf]的阳离子的相互作用位点是烷基氢而不是芳香氢;当水分子浓度较高时,水分子倾向于自身缔合形成小团簇结构,水分子与[emim][OTf]的阳离子的相互作用位点是芳香氢而不是烷基氢.     

Electron and Geometry Structure of Hydrogen-Bonded Complexes of Guanine with One Molecule Methanol. A DFT Level Study

Summary. The geometries, harmonic vibrational frequencies, and energies of eight hydrogen-bonded complexes of guanine with one molecule methanol are computed using the DFT (B3LYP) method together with the 6-31+G* basis functions. In the investigation two stable tautomers of guanine (oxo-amino N9H and oxo-amino N7H) were chosen. They were included in a variety of H-bonded complexes with one molecule methanol. In order to investigate the nature of the intermolecular bonds, the bonding energies and thermodynamic properties of the complexes were calculated.     

Electron and Geometry Structure of Hydrogen-Bonded Complexes of Guanine with One Molecule Methanol. A DFT Level Study

The geometries, harmonic vibrational frequencies, and energies of eight hydrogen-bonded complexes of guanine with one molecule methanol are computed using the DFT (B3LYP) method together with the 6-31+G* basis functions. In the investigation two stable tautomers of guanine (oxo-amino N9H and oxo-amino N7H) were chosen. They were included in a variety of H-bonded complexes with one molecule methanol. In order to investigate the nature of the intermolecular bonds, the bonding energies and thermodynamic properties of the complexes were calculated.